Peptide mapping by MALDI has been long used for protein identification of protein isolated by SDS-PAGE. For an efficient peptide mapping and consequent extraction of peptides containing cysteine we have investigated the use of several alkylating agents. Furthermore, we have shown that the use of labeled agents or the simultaneous use of two alkylating reagents allowed the identification of peptides containing cysteines among all the tryptic peptides. This information can be used to constrain the search in the data base if the protein is unknown. The methodology was applied and show to work with selected proteins. We are now in the process of applying this methods for the identification of proteins purified from the nuclear envelope.